[mitzimorris]

Submission Checklist

• Builds locally
• Declare copyright holder and open-source license: see below

Summary

Updated _output.yml files for all docs so that docs will build with bookdown 2.23. Unfortunately, bookdown 2.23 introduced a breaking change for the yaml headers w/r/t search engine config.

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company): Columbia University

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[mitzimorris]

this isn't quite ready to go. need to figure out how to address need for bookdown 2.23 - suggestions welcome.

[bob-carpenter]

I converted this to a draft (button under the Reviewers list) and added [WIP] to the title. Let us know when it's ready to review.

[mitzimorris]

Improved build.py script and added more info to README.md.

In order to check for bookdown 2.23 or greater, usingsubprocess.run which requires Python 3.5 or higher.

[mitzimorris]

this is ready for review.

[WardBrian]

I get an error straight off:

(r-env) [brian@FlatTop bookdowntest on use-bookdown-2-23] $ python build.py 2 27
Traceback (most recent call last):
  File "/home/brian/Dev/integration/bookdowntest/build.py", line 125, in <module>
    main()
  File "/home/brian/Dev/integration/bookdowntest/build.py", line 77, in main
    check_bookdown_2_23()
  File "/home/brian/Dev/integration/bookdowntest/build.py", line 39, in check_bookdown_2_23
    check = subprocess.run(command, capture_output=True, text=True)
  File "/home/brian/miniconda3/envs/r-env/lib/python3.9/subprocess.py", line 505, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/home/brian/miniconda3/envs/r-env/lib/python3.9/subprocess.py", line 951, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/brian/miniconda3/envs/r-env/lib/python3.9/subprocess.py", line 1821, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/Rscript'

The reason seems to be the hard coding of the Rscript path:

(r-env) [brian@FlatTop bookdowntest on use-bookdown-2-23] $ which Rscript
/home/brian/miniconda3/envs/r-env/bin/Rscript

[WardBrian]

While subprocess.run was added in 3.5, the capture_output kwarg wasn't until 3.7 -- I think that's probably fine, but we should correct the minimum version here.

[mitzimorris]

also checking in script itself.

[WardBrian]

Suggested change

	command = ["/usr/local/bin/Rscript", "-e", "utils::packageVersion(\"bookdown\") > 0.22"]
	command = ["Rscript", "-e", "utils::packageVersion(\"bookdown\") > 0.22"]

[mitzimorris]

doh! done!